predCrossMeanBVsOneTrait: predCrossMeanBVsOneTrait

In wolfemd/predCrossVar: Prediction of family genomic variances and covariances

Description

Predict the mean breeding value of each family, for a single trait, given parental allelic dosages and (posterior mean) marker effects. NOTE: Marker effects should represent allele substitution effects. Either by fitting an additive-only model OR an genotypic-partitioned additive+dominance model, with allele sub effects computed as a+d(q-p), where q and p are allele freqs in the training pop. used.

Usage

predCrossMeanBVsOneTrait(
  Trait,
  CrossesToPredict,
  doseMat,
  postMeanAlleleSubEffects
)

Arguments

Trait	string, label of trait (name in list of postMeanAddEffects) to compute
CrossesToPredict	data.frame or tibble, col/colnames: sireID, damID. sireID and damID must both be in the haploMat.
doseMat	dosage matrix. Assumes SNPs in M coded 0, 1, 2 (requires rounding dosages to integers). M is Nind x Mrow, numeric matrix, with row/colnames to indicate SNP/ind ID
postMeanAlleleSubEffects	list of named vectors (or column matrices) with the posterior mean ALLELE SUBSTITUTION marker effects.

Value

tibble with parental GEBV and the pred Mean GEBV (mean of parents) for each cross.

wolfemd/predCrossVar documentation built on Dec. 21, 2020, 10:14 a.m.